That's an ambiguous question in native English too and could only be fully, precisely understood from context. While I would interpret the sentence from only t

That's an ambiguous question in native English too and could only be fully, precisely understood from context. While I would interpret the sentence from only the context you provided in the way that you describe, I would characterize the question as unclear. A military chain of command would definitely phrase the question more like "Mr. President, can you confirm you are giving us the order to launch the nukes? Please present your confirmation code." But I understand what you mean about negations having opposite meanings in (spoken) English (where context is clearer). I consider that kind of negation and answer to be sloppy written grammar and something to avoid in written English.